6EZN: Yeast oligosaccharyltransferase (OST) complex
Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex. Determined by electron microscopy at 3.3 Å resolution. Released 17 Jan 2018.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 8
- Atoms
- 17,008
- Mol. weight
- 291.41 kDa
- Ligands
- CPL, PTY, NAG
- Released
- 17 Jan 2018
Explore 6EZN in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6EZN contains 69 α-helices and 100 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 4 helices, 37 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 32-41 | 10 | 1 |
| β-strand | 48-56 | 9 | 1 |
| β-strand | 66-70 | 5 | 2 |
| β-strand | 78-84 | 7 | 1 |
| β-strand | 93-96 | 4 | 2 |
| β-strand | 113-118 | 6 | 2 |
| β-strand | 128-137 | 10 | 1 |
| β-strand | 142-143 | 2 | 3 |
| β-strand | 147 | 1 | 4 |
| β-strand | 155-161 | 7 | 3 |
| β-strand | 170-172 | 3 | 1 |
| β-strand | 174-178 | 5 | 1 |
| β-strand | 183-185 | 3 | 3 |
| β-strand | 197-199 | 3 | 1 |
| β-strand | 202-205 | 4 | 1 |
| β-strand | 209-211 | 3 | 1 |
| β-strand | 219-225 | 7 | 3 |
| β-strand | 231-243 | 13 | 5 |
| β-strand | 248-259 | 12 | 5 |
| β-strand | 263 | 1 | 4 |
| α-helix | 270-279 | 10 | |
| β-strand | 288 | 1 | 6 |
| β-strand | 291-294 | 4 | 7 |
| β-strand | 303-305 | 3 | 5 |
| β-strand | 310 | 1 | 5 |
| β-strand | 314-317 | 4 | 7 |
| β-strand | 320-323 | 4 | 7 |
| β-strand | 329 | 1 | 6 |
| β-strand | 334-344 | 11 | 5 |
| α-helix | 345-347 | 3 | |
| β-strand | 349-351 | 3 | 8 |
| β-strand | 358-364 | 7 | 8 |
| β-strand | 372-374 | 3 | 5 |
| β-strand | 377-383 | 7 | 5 |
| β-strand | 388-393 | 6 | 8 |
| β-strand | 400-406 | 7 | 5 |
| β-strand | 416-423 | 8 | 5 |
| β-strand | 426-427 | 2 | 5 |
| β-strand | 434-440 | 7 | 8 |
| α-helix | 443-446 | 4 | |
| α-helix | 448-466 | 19 | |
Chain B: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-40 | 17 | |
| α-helix | 42-67 | 26 | |
| α-helix | 75-99 | 25 | |
| α-helix | 109-128 | 20 | |
Chain C: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 218-232 | 15 | |
| α-helix | 236-240 | 5 | |
| α-helix | 269-289 | 21 | |
| α-helix | 291-297 | 7 | |
| α-helix | 305-334 | 30 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-31 | 28 | |
Chain E: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-11 | 9 | |
| β-strand | 14-15 | 2 | 8 |
| α-helix | 25-41 | 17 | |
| α-helix | 53-81 | 29 | |
Chain F: 32 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| α-helix | 48-60 | 13 | |
| α-helix | 63-67 | 5 | |
| α-helix | 90-99 | 10 | |
| α-helix | 100-104 | 5 | |
| α-helix | 111-116 | 6 | |
| β-strand | 117 | 1 | 9 |
| α-helix | 119-137 | 19 | |
| α-helix | 140-152 | 13 | |
| α-helix | 154-157 | 4 | |
| β-strand | 163 | 1 | 9 |
| α-helix | 172-188 | 17 | |
| α-helix | 191-205 | 15 | |
| α-helix | 211-216 | 6 | |
| α-helix | 218-227 | 10 | |
| α-helix | 233-249 | 17 | |
| α-helix | 259-262 | 4 | |
| α-helix | 267-286 | 20 | |
| α-helix | 291-294 | 4 | |
| α-helix | 356-362 | 7 | |
| α-helix | 370-378 | 9 | |
| α-helix | 385-401 | 17 | |
| α-helix | 406-427 | 22 | |
| α-helix | 442-473 | 32 | |
| α-helix | 495-505 | 11 | |
| β-strand | 512-513 | 2 | 10 |
| α-helix | 517-519 | 3 | |
| α-helix | 520-526 | 7 | |
| β-strand | 530-531 | 2 | 10 |
| α-helix | 540-550 | 11 | |
| α-helix | 554-563 | 10 | |
| β-strand | 568-572 | 5 | 10 |
| α-helix | 588-595 | 8 | |
| β-strand | 604 | 1 | 11 |
| β-strand | 606 | 1 | 11 |
| α-helix | 622-625 | 4 | |
| α-helix | 628-633 | 6 | |
| β-strand | 642 | 1 | 12 |
| β-strand | 645 | 1 | 12 |
| β-strand | 646-647 | 2 | 13 |
| β-strand | 654-655 | 2 | 13 |
| β-strand | 666-671 | 6 | 10 |
| β-strand | 677-682 | 6 | 10 |
| α-helix | 683-686 | 4 | |
| α-helix | 692-698 | 7 | |
Chain G: 12 helices, 36 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-31 | 4 | 14 |
| β-strand | 35 | 1 | 14 |
| α-helix | 38-40 | 3 | |
| α-helix | 41-49 | 9 | |
| β-strand | 56-59 | 4 | 14 |
| α-helix | 65-66 | 2 | |
| β-strand | 69 | 1 | 15 |
| β-strand | 74 | 1 | 15 |
| β-strand | 78-81 | 4 | 14 |
| α-helix | 89-93 | 5 | |
| α-helix | 96-103 | 8 | |
| β-strand | 108-112 | 5 | 14 |
| β-strand | 114 | 1 | 16 |
| β-strand | 117 | 1 | 16 |
| α-helix | 120-128 | 9 | |
| β-strand | 131-133 | 3 | 17 |
| β-strand | 139-142 | 4 | 18 |
| β-strand | 151-154 | 4 | 19 |
| α-helix | 155-157 | 3 | |
| β-strand | 158 | 1 | 20 |
| β-strand | 171-174 | 4 | 19 |
| β-strand | 177 | 1 | 21 |
| β-strand | 180-182 | 3 | 17 |
| β-strand | 188-190 | 3 | 14 |
| β-strand | 192 | 1 | 20 |
| β-strand | 198-201 | 4 | 18 |
| α-helix | 206-208 | 3 | |
| β-strand | 216 | 1 | 17 |
| β-strand | 218-222 | 5 | 14 |
| β-strand | 228-232 | 5 | 14 |
| β-strand | 234 | 1 | 21 |
| α-helix | 248-257 | 10 | |
| β-strand | 264-266 | 3 | 22 |
| β-strand | 270-273 | 4 | 22 |
| β-strand | 285 | 1 | 23 |
| β-strand | 289-299 | 11 | 22 |
| β-strand | 304-306 | 3 | 22 |
| β-strand | 313-317 | 5 | 24 |
| β-strand | 321-326 | 6 | 24 |
| β-strand | 328 | 1 | 22 |
| β-strand | 337-340 | 4 | 22 |
| β-strand | 344-345 | 2 | 22 |
| α-helix | 346-347 | 2 | |
| β-strand | 351-359 | 9 | 24 |
| β-strand | 367-375 | 9 | 24 |
| β-strand | 376 | 1 | 23 |
| α-helix | 377-379 | 3 | |
| α-helix | 393-415 | 23 | |
Chain H: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-34 | 5 | 25 |
| β-strand | 44 | 1 | 26 |
| β-strand | 68-70 | 3 | 25 |
| α-helix | 77-78 | 2 | |
| β-strand | 82-86 | 5 | 26 |
| β-strand | 87 | 1 | 27 |
| β-strand | 92 | 1 | 27 |
| β-strand | 95-96 | 2 | 26 |
| β-strand | 101-103 | 3 | 28 |
| β-strand | 106-108 | 3 | 28 |
| β-strand | 111-114 | 4 | 25 |
| α-helix | 122-128 | 7 | |
| β-strand | 134-138 | 5 | 26 |
| β-strand | 151-156 | 6 | 26 |
| β-strand | 180 | 1 | 24 |
| α-helix | 183-189 | 7 | |
| α-helix | 193-212 | 20 | |
| α-helix | 213-217 | 5 | |
| α-helix | 231-252 | 22 | |
| α-helix | 257-271 | 15 | |
| α-helix | 277-281 | 5 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 | A | protein | 476 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P41543 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 | B | protein | 130 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P46964 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 | C | protein | 350 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P48439 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 | D | protein | 36 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q99380 (AlphaFold model) |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 | E | protein | 86 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q92316 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 | F | protein | 718 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P39007 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 | G | protein | 430 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33767 |
| Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 | H | protein | 286 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q02795 |
Sequence of entity 1 (A), FASTA
>6EZN_1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 (chains A)
MRQVWFSWIVGLFLCFFNVSSAAQYEPPATWENVDYKRTIDVSNAYISETIEITIKNIAS
EPATEYFTAFESGIFSKVSFFSAYFTNEATFLNSQLLANSTTAPGDDGESEIRYGIIQFP
NAISPQEEVSLVIKSFYNTVGIPYPEHVGMSEEQHLLWETNRLPLSAYDTKKASFTLIGS
SSFEEYHPPNDESLLGKANGNSFEFGPWEDIPRFSSNETLAIVYSHNAPLNQVVNLRRDI
WLSHWASTIQFEEYYELTNKAAKLSKGFSRLELMKQIQTQNMRQTHFVTVLDMLLPEGAT
DHYFTDLVGLVSTSHAERDHFFIRPRFPIFGGWNYNFTVGWTNKLSDFLHVSSGSDEKFV
ASIPILNGPPDTVYDNVELSVFLPEGAEIFDIDSPVPFTNVSIETQKSYFDLNKGHVKLT
FSYRNLISQVANGQVLIKYDYPKSSFFKKPLSIACYIFTALMGVFVLKTLNMNVTN
Sequence of entity 2 (B), FASTA
>6EZN_2 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2 (chains B)
MAKAPKANTPKVTSTSSAVLTDFQETFKTSKRAYFAQIEKYPKLKLIDTFCFFLVLLGVI
QCTFIILIRDNFPFNAFLAGFIICVGQFVLLMSLRLQLCNSFPGISKNRAFAEFIVASLI
LHFVCLHFIN
Sequence of entity 3 (C), FASTA
>6EZN_3 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3 (chains C)
MNWLFLVSLVFFCGVSTHPALAMSSNRLLKLANKSPKKIIPLKDSSFENILAPPHENAYI
VALFTATAPEIGCSLCLELESEYDTIVASWFDDHPDAKSSNSDTSIFFTKVNLEDPSKTI
PKAFQFFQLNNVPRLFIFKPNSPSILDHSVISISTDTGSERMKQIIQAIKQFSQVNDFSL
HLPMDWTPIITSTIITFITVLLFKKQSKLMFSIISSRIIWATLSTFFIICMISAYMFNQI
RNTQLAGVGPKGEVMYFLPNEFQHQFAIETQVMVLIYGTLAALVVVLVKGIQFLRSHLYP
ETKKAYFIDAILASFCALFIYVFFAALTTVFTIKSPAYPFPLLRLSAPFK
Sequence of entity 4 (D), FASTA
>6EZN_4 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4 (chains D)
MISDEQLNSLAITFGIVMMTLIVIYHAVDSTMSPKN
Sequence of entity 5 (E), FASTA
>6EZN_5 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5 (chains E)
MTYEQLYKEFHSSKSFQPFIHLDTQPKFAICGLIVTLAVLSSALFAVGSKSSYIKKLFFY
TILSVIGSLFAGLTTVFASNSFGVYV
Sequence of entity 6 (F), FASTA
>6EZN_6 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 (chains F)
MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVN
NSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAP
LFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFM
FWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYT
TWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMV
SLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFF
FDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVA
LSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVV
LPSQTPDGKLALIDDFREAYYWLRMNSDEDSKVAAWWDYGYQIGGMADRTTLVDNNTWNN
THIAIVGKAMASPEEKSYEILKEHDVDYVLVIFGGLIGFGGDDINKFLWMIRISEGIWPE
EIKERDFYTAEGEYRVDARASETMRNSLLYKMSYKDFPQLFNGGQATDRVRQQMITPLDV
PPLDYFDEVFTSENWMVRIYQLKKDDAQGRTLRDVGELTRSSTKTRRSIKRPELGLRV
Sequence of entity 7 (G), FASTA
>6EZN_7 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1 (chains G)
MRTDWNFFFCILLQAIFVVGTQTSRTLVLYDQSTEPLEEYSVYLKDLEQRNYKLEYLDIN
STSTTVDLYDKEQRLFDNIIVFPTKGGKNLARQIPVKQLIKFFENEGNILCMSSPGAVPN
TIRLFLNELGIYPSPKGHVIRDYFSPSSEELVVSSNHLLNKYVYNARKSEDFVFGESSAA
LLENREQIVPILNAPRTSFTESKGKCNSWTSGSQGFLVVGFQNLNNARLVWIGSSDFLKN
KNQDSNQEFAKELLKWTFNEKSVIKSVHAVHSHADGTSYDEEPYKIKDKVIYSVGFSEWN
GEEWLPHIADDIQFELRQVDPYYRLTLSPSGNDSETQYYTTGEFILPDRHGVFTFLTDYR
KIGLSFTTDKDVKAIRHLANDEYPRSWEISNSWVYISAICGVIVAWIFFVVSFVTTSSVG
KKLETFKKTN
Sequence of entity 8 (H), FASTA
>6EZN_8 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1 (chains H)
MQFFKTLAALVSCISFVLAYVAQDVHVSFPSTAGKSRVMIGKVEPRIGIDETVPTTITVE
DPNEVIQVNFAIESTNKPFQNTLLIGLPNKNLEMAFEPEIKDNGKLSMYKYRIDLAKLDA
ALLQEASRSPEPIKATLILASSTAKPKENLFREILQLNLNFDVDHSDSSLVDKFGIKPEI
HHIFHAEPKRVAKPIAVIFVLIIFITILSLIVTWLNSCAAAFNNIPTGVTAVYFLGFIAT
IVGFEVIFARYYLGTSIFETLFSSLYLGAPGLLTSTKFLRSFGQTI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CPL | 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine | C42 H80 N O8 P | 4 |
| PTY | Phosphatidylethanolamine | C40 H80 N O8 P | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
Primary citation
Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation. Wild, R., Kowal, J., Eyring, J. et al. Science (2018) 359:545-550. DOI 10.1126/science.aar5140 · PubMed
Other PDB entries of the same protein (UniProt P41543 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8AGE 2.8 Å, Structure of yeast oligosaccharylransferase complex with acceptor peptide bound
- 8AGB 3.0 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
- 8AGC 3.1 Å, Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide…
- 7OCI 3.46 Å, Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex
- 6C26 3.5 Å, The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex
Browse structure collections
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